Gen-EpiX 0.0.1__tar.gz

gen_epix-0.0.1/Gen_EpiX.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: Gen-EpiX
+Version: 0.0.1
+Summary: Genomic Epidemiology platform for disease X
+Author-email: RIVM-bioinformatics <ids-bioinformatics@rivm.nl>
+License-Expression: EUPL-1.2
+Project-URL: Homepage, https://github.com/RIVM-bioinformatics/Gen-EpiX
+Project-URL: Documentation, https://rivm-bioinformatics.github.io/Gen-EpiX/
+Keywords: Genomic Epidemiology,Disease X,Bioinformatics
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastapi[standard]==0.115.5
+Requires-Dist: uvicorn==0.32.1
+Requires-Dist: gunicorn==21.2.*
+Requires-Dist: starlette==0.41.3
+Requires-Dist: httpx==0.27.2
+Requires-Dist: python-jose==3.3.0
+Requires-Dist: sqlalchemy==2.0.36
+Requires-Dist: sqlalchemy_utils==0.41.2
+Requires-Dist: sqlmodel==0.0.22
+Requires-Dist: pydantic==2.7.*
+Requires-Dist: pandas==2.2.3
+Requires-Dist: ulid-py==1.1.0
+Requires-Dist: fire==0.7.0
+Requires-Dist: dynaconf==3.2.6
+Requires-Dist: scipy==1.14.1
+Requires-Dist: numpy==2.1.3
+Requires-Dist: biopython==1.84
+Requires-Dist: cachetools==5.5.0
+Requires-Dist: slowapi==0.1.9
+Provides-Extra: dependencies
+Requires-Dist: pytest; extra == "dependencies"
+Requires-Dist: pytest-cov; extra == "dependencies"
+Requires-Dist: pytest-mock; extra == "dependencies"
+Requires-Dist: pytest-dependency; extra == "dependencies"
+Requires-Dist: pyinstrument; extra == "dependencies"
+Requires-Dist: isort; extra == "dependencies"
+Requires-Dist: black; extra == "dependencies"
+Requires-Dist: pylint; extra == "dependencies"
+Requires-Dist: mypy; extra == "dependencies"
+Requires-Dist: cryptography; extra == "dependencies"
+Requires-Dist: pandas-stubs; extra == "dependencies"
+Requires-Dist: types-openpyxl; extra == "dependencies"
+Requires-Dist: types-cachetools; extra == "dependencies"
+Requires-Dist: types-python-jose; extra == "dependencies"
+Dynamic: license-file
+
+<p align="center">
+    <img src="docs/assets/Gen-epix-logo.svg" alt="lsp-api-logo">
+</p>
+<p align="center">
+    <em>Genomic Epidemiology platform for disease X</em>
+</p>
+<p align="center">
+    <a href="https://github.com/RIVM-bioinformatics/lsp-api/actions/workflows/main.yml/badge.svg" target="_blank">
+        <img src="https://github.com/RIVM-bioinformatics/lsp-api/actions/workflows/main.yml/badge.svg" alt="tests">
+    </a>
+    <a href="https://sonarcloud.io/api/project_badges/measure?project=RIVM-bioinformatics_lsp-api&metric=alert_status&token=51a6c8d13bac07e815053949f389fe38db584061" target="_blank">
+        <img src="https://sonarcloud.io/api/project_badges/measure?project=RIVM-bioinformatics_lsp-api&metric=alert_status&token=51a6c8d13bac07e815053949f389fe38db584061" alt="sonarqube">
+    </a>
+    <a href="https://sonarcloud.io/api/project_badges/measure?project=RIVM-bioinformatics_lsp-api&metric=coverage&token=51a6c8d13bac07e815053949f389fe38db584061" target="_blank">
+        <img src="https://sonarcloud.io/api/project_badges/measure?project=RIVM-bioinformatics_lsp-api&metric=coverage&token=51a6c8d13bac07e815053949f389fe38db584061" alt="coverage">
+    </a>
+</p>
+
+
+
+---
+
+**Source Code**: <a href="https://github.com/RIVM-bioinformatics/lsp-api" target="_blank">https://github.com/RIVM-bioinformatics/lsp-api</a>
+
+---
+# Gen-EpiX: Genomic Epidemiology platform for disease X (beta version)
+
+Gen-EpiX is platform for visualizing and analyzing genomic epidemiology data. It has fine-grained access controls for collaboration between multiple organizations.
+
+## Key Features
+
+- **Visualisation**: Visualize cases by time, place, person and also by genome through a phylogenetic tree coupled to the cases.
+- **Fine-grained access**: Give different organizations different access rights per disease, down to individual variables. Organizations can manage access of their own users by themselves.
+- **Search**: Search and filter cases, including on genetic similarity.
+- **Signal detection**: Detect, define and share sets of cases, signals and outbreaks.
+- **Disease X**: Any disease and corresponding analysis variables can be added.
+- **Data**: Adheres to the Medallion data architecture design pattern. The silver layer consists of normalized and standardized patient or subject data compliant with <a href="https://www.ohdsi.org/data-standardization" target="_blank">OMOP Common Data Model</a>, and a dedicated database for genetic sequence data and computation of phylogenetic trees. The gold layer consists of case data ready for analysis in the form of a single row of data per case.
+- **Tech**: OpenAPI compliant API, deployable on cloud or on-premise, support for multiple authentication providers. Python/FastAPI backend and default TypeScript/React frontend available from gen-epix-web.
+
+## Deliberately not in scope
+
+- **Disease-specific knowledge**: Every organization has their own variables that are important for analysis, as well as their own bioinformatics to process genetic sequence data. We therefore avoided any disease-specific code both for the generation of these data and for the analysis variables that can be defined. Only the results are stored. 
+- **Collaboration-specific knowledge**: Every collaboration or country (e.g. for public health surveillance of diseases) has their own specifics in terms of access rights and any relevant geographic regions. We therefore avoided any country-specific code, both for the type of organizations that have access, and for any geographic data. 
+
+---
+
+# Installation 
+
+Below is a streamlined installation guide for various platforms:
+
+1. Install ODBC development headers:
+   ```console
+   sudo apt-get update
+   sudo apt-get install -y unixodbc-dev
+   ```
+
+2. Create and activate a conda environment:
+   ```console
+   conda create --name gen-epix python=3.12
+   conda activate gen-epix
+   ```
+
+3. Install dependencies*:
+   ```console
+   pip install -r requirements.txt
+   pip install --no-binary :all: pyodbc==5.2.*
+   ```
+   **Some hardware architectures (especially Apple M1/M2/M3 chips) require pyodbc to be compiled from source for compatibility*
+<br>
+
+4. For development, add testing tools:
+   ```console
+   pip install -r dev-requirements.txt
+   ```
+
+
+**SSL Certificate Setup**
+
+1. Install mkcert:
+   ```console
+   # Linux
+   sudo apt install mkcert
+   
+   # macOS
+   brew install mkcert
+   ```
+
+2. Generate certificates:
+   ```console
+   mkcert -install
+   mkcert -key-file key.pem -cert-file cert.pem localhost 127.0.0.1
+   ```
+
+3. Copy the generated files:
+   ```console
+   cp key.pem cert.pem /path/to/project/cert/
+   ```
+
+4. For WSL users: Run the commands in Windows PowerShell and copy files to both the project cert directory and your WSL home directory.
+
+---
+
+## Usage
+
+### Starting the API
+
+1. Activate the conda environment:
+```console
+conda activate gen-epix
+```
+2. Run the application:
+```console
+python run.py [service] [app_type] [env_name] [idp_config]
+```
+- `service`: The service to run (api, etl) 
+- `app_type`: Specific configuration for an app type (casedb, seqdb, omopbd)
+- `env_name`: Name of the environment.
+-  `idp_config`: Which authentication setting to use (idps, mock_idps, no_auth, debug, no_ssl)
+
+---
+
+### Example
+
+```console
+conda activate gen-epix
+python run.py api casedb local idps
+```
+
+<img src="docs/assets/example_docs.png" alt="example-docs">
+
+---
+
+## Dependencies
+
+Gen-EpiX relies on several Python packages to provide its functionality:
+
+**Core Dependencies**
+* <a href="https://fastapi.tiangolo.com" target="_blank"><code>fastapi</code></a> - Modern, high-performance web framework
+* <a href="https://www.sqlalchemy.org" target="_blank"><code>sqlalchemy</code></a> - SQL toolkit and Object-Relational Mapping (ORM) library
+* <a href="https://docs.pydantic.dev" target="_blank"><code>pydantic</code></a> - Data validation and settings management
+* <a href="https://biopython.org" target="_blank"><code>biopython</code></a> - Tools for computational molecular biology
+
+**Database Connectors**
+* <a href="https://github.com/mkleehammer/pyodbc" target="_blank"><code>pyodbc</code></a> - ODBC database adapter
+
+**API Server**
+* <a href="https://www.uvicorn.org" target="_blank"><code>uvicorn</code></a> - ASGI web server
+
+**Development Tools**
+* <a href="https://docs.pytest.org" target="_blank"><code>pytest</code></a> - Testing framework
+* <a href="https://black.readthedocs.io" target="_blank"><code>black</code></a> - Code formatter
+* <a href="https://pylint.org" target="_blank"><code>pylint</code></a> - Static code analyzer
+* <a href="https://mypy.readthedocs.io" target="_blank"><code>mypy</code></a> - Static type checker
+
+For a complete list of dependencies, refer to:
+- [requirements.txt](requirements.txt) - Production dependencies
+- [dev-requirements.txt](dev-requirements.txt) - Development dependencies
+
+**Python Version**
+Gen-EpiX requires Python 3.12 or higher.

gen_epix-0.0.1/Gen_EpiX.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+Gen_EpiX.egg-info/PKG-INFO
+Gen_EpiX.egg-info/SOURCES.txt
+Gen_EpiX.egg-info/dependency_links.txt
+Gen_EpiX.egg-info/requires.txt
+Gen_EpiX.egg-info/top_level.txt
+gen_epix/__init__.py
+gen_epix/casedb/__init__.py
+gen_epix/casedb/app.py
+gen_epix/casedb/app_setup.py
+gen_epix/casedb/env.py
+gen_epix/casedb/api/abac.py
+gen_epix/casedb/api/auth.py
+gen_epix/casedb/api/base.py
+gen_epix/casedb/api/case.py
+gen_epix/casedb/api/geo.py
+gen_epix/casedb/api/model.py
+gen_epix/casedb/api/ontology.py
+gen_epix/casedb/api/organization.py
+gen_epix/casedb/api/rbac.py
+gen_epix/casedb/api/router.py
+gen_epix/casedb/api/system.py
+gen_epix/casedb/config/__init__.py
+gen_epix/casedb/config/logging.debug.yaml
+gen_epix/casedb/config/logging.yaml
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+gen_epix/casedb/config/settings.toml
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+gen_epix/casedb/config/.secret/db
+gen_epix/casedb/config/.secret/log
+gen_epix/casedb/config/.secret/repository-sasql-defaults
+gen_epix/casedb/config/.secret/root-organization
+gen_epix/casedb/config/.secret/root-user
+gen_epix/casedb/config/idp/identity_providers.json
+gen_epix/casedb/config/idp/mock_identity_provider.json
+gen_epix/casedb/config/idp/no_identity_providers.json
+gen_epix/casedb/domain/__init__.py
+gen_epix/casedb/domain/enum.py
+gen_epix/casedb/domain/exc.py
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+gen_epix/casedb/domain/command/crud.py
+gen_epix/casedb/domain/command/non_crud.py
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+gen_epix/casedb/domain/model/ontology.py
+gen_epix/casedb/domain/model/organization.py
+gen_epix/casedb/domain/model/seqdb.py
+gen_epix/casedb/domain/model/subject.py
+gen_epix/casedb/domain/model/system.py
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+gen_epix/casedb/domain/model/abac/abac.py
+gen_epix/casedb/domain/model/abac/case_abac.py
+gen_epix/casedb/domain/model/case/__init__.py
+gen_epix/casedb/domain/model/case/case.py
+gen_epix/casedb/domain/model/case/complete_case_type.py
+gen_epix/casedb/domain/policy/__init__.py
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+gen_epix/casedb/domain/policy/rbac.py
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gen_epix-0.0.1/Gen_EpiX.egg-info/dependency_links.txt

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gen_epix-0.0.1/Gen_EpiX.egg-info/requires.txt

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gen_epix-0.0.1/Gen_EpiX.egg-info/top_level.txt

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